Rice straw is supposed to be an environment-friendly biomaterial for inhibiting the growth of harmful blooms of the cyanobacterium Microcystis aeruginosa. However, its potential mechanism is not well known. To explore this mechanism, the growth, cell viability (esterase activity, membrane potential, and membrane integrity), photosynthesis, and cell size of M. aeruginosa were determined using flow cytometry and Phyto-PAM after exposure to rice straw extracts (RSE). The results show that doses from 2.0 to 10.0 g/L of RSE efficiently inhibited the alga for 15 days, while the physiologic and morphologic responses of the cyanobacteria were time-dependent. RSE interfered with the cell membrane potential, cell size, and in vivo chlorophyll-a fluorescence on the first day. After 7 days of exposure, RSE was transported into the cytosol, which disrupted enzyme activity and photosynthesis. The cyanobacteria then started to repair its physiology (enzyme activity, photosynthesis) and remained viable, suggesting that rice straw act as an algistatic agent.